Brisbane City Council employees have voted overwhelmingly in support of a new pay deal.

The official acceptance of the new enterprise bargaining agreement, which will be in place until October 2020, came after repeated industrial action by staff, including bus drivers, who offered free travel to commuters.

After an independently administered council-wide vote, which was finalised on Friday, 89 per cent of all employees who had their say voted to support the EBA.

The agreement includes a $500 one-off sign-off payment for staff, and annual 2.5 per cent pay rises.

Brisbane City Council reached a wage deal with drivers in September.

Brisbane Lord Mayor Graham Quirk said in February that the civic cabinet approved an automatic 2.5 per cent wage increase, "as it was clear that EBA negotiations were still some time from being finalised".